Please note that ally lists are not reciprocal, in other words it is possible for a race to appear as allies of another race, while not having that race in their own ally list. This simply reflects the fact that to get a race as an ally there must be a good chance of a small contingent of their troops serving in a large army of troops drawn from the main list. In the case of Dark Elves and Skaven, for example, it seemed sensible to me (Jervis) that small contingents of Dark Elves could serve in a Skaven army, but not vice-versa.
Characters can join either unit, but note that they do not benefit from either troops types special rules. Thus a character with the Scouts can't infiltrate, and a character with the Dark Riders can't make a free march move at the start of the battle or fire and flee. As a house rule I recommend that you allow Champions belonging to such units to benefit from the troops special abilities (so a Scout Champion could infiltrate, for example).
No. Magic weapons never benefit from special rules that apply to a 'mundane' weapon. This is an expansion of the rules for magic weapons found on page 39 of Battle Magic.